Use em, yes, but meanwhile "px" should have continued to mean "pixel", not "96th of an inch except on mobile where ...". Occasionally you really do need to talk about pixels in CSS, and redefining "px" makes that impossible.

I was at the same time telling myself that we really need to start using em more often. I have used px so many times at this point because it's more convenient for precise aligning. This is actually going to be a problem considering retina display macbooks might be coming soon.

It's not going to be a problem, precisely because a "px" in CSS doesn't mean an actual device pixel.

And that's because we've had "retina" devices for many years now, called "printers" and CSS was designed to deal with that situation from the start.